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基于bwa，做一些优化，注释
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C 90.9%
JavaScript 3.5%
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C++ 0.9%
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Heng Li 8f89f55484 fixed a segfault when there are too few good bases. 2011-11-17 22:13:38 -05:00
.gitignore Added barcode support 2011-01-15 15:35:39 -05:00
COPYING Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
ChangeLog Update to the latest modfication 0.5.9rc1-2. Update ChangeLog 2011-01-13 20:54:10 -05:00
Makefile mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
NEWS Release BWA-0.6.0 2011-11-12 20:04:39 -05:00
QSufSort.c move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
QSufSort.h move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
README added SEAL 2011-11-12 20:48:35 -05:00
bamlite.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bamlite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bntseq.c fixed a segfault when there are too few good bases. 2011-11-17 22:13:38 -05:00
bntseq.h fixed a minor issue about +/-1 2011-10-25 13:00:41 -04:00
bwa.1 updated manual 2011-11-12 18:35:04 -05:00
bwape.c crash under non-typical setting (by John Marshall) 2011-11-12 16:53:53 -05:00
bwase.c fixed a minor issue about +/-1 2011-10-25 13:00:41 -04:00
bwase.h PE seems working; more testing needed 2011-10-20 17:45:41 -04:00
bwaseqio.c Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y 2011-07-10 17:04:06 +02:00
bwt.c fixed a typo 2011-11-02 09:03:05 -04:00
bwt.h forward-backward search seems working 2011-10-25 12:31:36 -04:00
bwt_gen.c print msg to stderr; output more in fastmap 2011-10-25 15:06:13 -04:00
bwt_lite.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwt_lite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtaln.c bugfix: bwa-short MT does not work (by Peter) 2011-11-12 16:54:38 -05:00
bwtaln.h bugfix: integer overflow and strand error in sampe 2011-10-24 17:07:12 -04:00
bwtgap.c aln seems working 2011-10-20 16:13:35 -04:00
bwtgap.h aln seems working 2011-10-20 16:13:35 -04:00
bwtindex.c use forward-only pac to reduce memory 2011-10-21 12:03:14 -04:00
bwtio.c make changes to bwt.c 2011-10-19 17:42:42 -04:00
bwtmisc.c removed reverse pac; bwa is not working right now 2011-10-20 12:09:35 -04:00
bwtsw2.h bugfix: wrong mapping quality 2011-11-12 12:12:45 -05:00
bwtsw2_aux.c fixed a segfault when there are too few good bases. 2011-11-17 22:13:38 -05:00
bwtsw2_chain.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtsw2_core.c mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
bwtsw2_main.c bwasw: read and align two fastq at a time 2011-11-05 14:00:01 -04:00
bwtsw2_pair.c multithreading works again 2011-11-12 16:50:58 -05:00
cs2nt.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
fastmap.c drop smem based mapping algorithm 2011-10-27 10:56:09 -04:00
is.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
khash.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kseq.h Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa" 2011-07-10 16:40:42 +02:00
ksort.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kstring.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kstring.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
ksw.c mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
ksw.h mate rescue seems working (not MT) 2011-11-06 16:20:40 -05:00
kvec.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
main.c fixed a segfault when there are too few good bases. 2011-11-17 22:13:38 -05:00
main.h added bidirectional bwt; seems buggy 2011-10-25 00:22:28 -04:00
pairsam.pl pair two single-end SAMs 2011-11-05 10:56:25 -04:00
qualfa2fq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
simple_dp.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
solid2fastq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c multithreading works again 2011-11-12 16:50:58 -05:00
utils.h multithreading works again 2011-11-12 16:50:58 -05:00
xa2multi.pl Bugfix: reverse (complement) sequence and phred string if alternative alignment has different orientation than primary alignment 2011-09-07 14:31:28 +02:00

README 

Released packages can be downloaded from SourceForge.net:

  http://sourceforge.net/projects/bio-bwa/files/

Introduction and FAQ are available at:

  http://bio-bwa.sourceforge.net

Manual page at:

  http://bio-bwa.sourceforge.net/bwa.shtml

Mailing list:

  bio-bwa-help@lists.sourceforge.net

To sign up:

  http://sourceforge.net/mail/?group_id=276243

Publications (Open Access):

  http://www.ncbi.nlm.nih.gov/pubmed/20080505
  http://www.ncbi.nlm.nih.gov/pubmed/19451168

Incomplete list of citations (via HubMed.org):

  http://www.hubmed.org/references.cgi?uids=20080505
  http://www.hubmed.org/references.cgi?uids=19451168

Related projects:

  http://pbwa.sourceforge.net/
  http://www.many-core.group.cam.ac.uk/projects/lam.shtml
  http://biodoop-seal.sourceforge.net/
  http://gitorious.org/bwa-cuda